hello，I am a QIIME2 beginner. I came up with difficulties these days.
when I running q2-picrust2 plugin, something strange happened.
The command I entered was：
qiime picrust2 full-pipeline --i-table dada2-table.qza --i-seq dada2-repset-seqs.qza --p-threads 12 --o-ko-metagenome ko.qza --o-ec-metagenome ec.qza --o-pathway-abundance pathway.qza
and then， nothing running.
So I added -- verbose to show the details, but it also failed.
Error running this command:
place_seqs.py --study_fasta /tmp/tmp4a2b4ytt/seqs.fna --ref_dir /home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref --out_tree /tmp/tmp4a2b4ytt/picrust2_out/out.tre --processes 12 --intermediate /tmp/tmp4a2b4ytt/picrust2_out/intermediate/place_seqs --min_align 0.8 --chunk_size 5000 --placement_tool epa-ng
Standard error of the above failed command:
Error running this command:
epa-ng --tree /home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --ref-msa /tmp/tmp4a2b4ytt/picrust2_out/intermediate/place_seqs/ref_seqs_hmmalign.fasta --query /tmp/tmp4a2b4ytt/picrust2_out/intermediate/place_seqs/study_seqs_hmmalign.fasta --chunk-size 5000 -T 12 -m /home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model -w /tmp/tmp4a2b4ytt/picrust2_out/intermediate/place_seqs/epa_out --filter-acc-lwr 0.99 --filter-max 100
Standard output of the above failed command:
INFO Selected: Output dir: /tmp/tmp4a2b4ytt/picrust2_out/intermediate/place_seqs/epa_out/
INFO Selected: Query file: /tmp/tmp4a2b4ytt/picrust2_out/intermediate/place_seqs/study_seqs_hmmalign.fasta
INFO Selected: Tree file: /home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre
INFO Selected: Reference MSA: /tmp/tmp4a2b4ytt/picrust2_out/intermediate/place_seqs/ref_seqs_hmmalign.fasta
INFO Selected: Filtering by accumulated threshold: 0.99
INFO Selected: Maximum number of placements per query: 100
INFO Selected: Automatic switching of use of per rate scalers
INFO Selected: Preserving the root of the input tree
INFO Selected: Specified model file: /home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model
INFO Selected: Reading queries in chunks of: 5000
INFO Selected: Using threads: 12
INFO ______ ____ ___ _ __ ______
/ // __ \ / | / | / // /
/ __/ / // // /| | ______ / |/ // / __
/ / / // ___ |/_____// /| // // /
/_____/// // || // |/ __/ (v0.3.8)
INFO Using model parameters:
INFO Rate heterogeneity: GAMMA (4 cats, mean), alpha: 0.453141 (user), weights&rates: (0.25,0.0250674) (0.25,0.220229) (0.25,0.782933) (0.25,2.97177)
Base frequencies (user): 0.229585 0.22008 0.298596 0.251739
Substitution rates (user): 1.00319 2.79077 1.5301 0.87441 3.83966 1
INFO Output file: /tmp/tmp4a2b4ytt/picrust2_out/intermediate/place_seqs/epa_out/epa_result.jplace
It really makes me wonder, is this because my computer doesn't have enough ram? Or other reasons?